Yes I'm having the same problem.
It might be possible that the state of whether the setup has been done or not is saved in the .kobo folder. So once you have set it up just make a copy of all its flash content, including the .kobo folder.
After a factory reset, all you will have to do is just restore all the content (delete the 2 pre-existing folders beginning with '.' first).
I have't tried it yet, but I will as soon as I get my hands on a Windows machine.

I just upgraded from 1.9.11 to 1.9.16, and was forced to create an account with the desktop app (yuck). I used the 2.1.6 desktop app under Wine.

First, though, I backed up my .kobo directory. Afterwards, I diff-ed the new and old .kobo directories.